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- PDB-4yup: Multiconformer fixed-target X-ray free electron (XFEL) model of C... -

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Basic information

Entry
Database: PDB / ID: 4yup
TitleMulticonformer fixed-target X-ray free electron (XFEL) model of CypA at 273 K
ComponentsPeptidyl-prolyl cis-trans isomerase A
KeywordsISOMERASE / Cyclophilin
Function / homology
Function and homology information


negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / negative regulation of viral life cycle / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / virion binding / negative regulation of stress-activated MAPK cascade ...negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / negative regulation of viral life cycle / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / virion binding / negative regulation of stress-activated MAPK cascade / endothelial cell activation / Basigin interactions / protein peptidyl-prolyl isomerization / cyclosporin A binding / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / Early Phase of HIV Life Cycle / Integration of provirus / negative regulation of protein phosphorylation / APOBEC3G mediated resistance to HIV-1 infection / viral release from host cell / Calcineurin activates NFAT / activation of protein kinase B activity / Binding and entry of HIV virion / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / neutrophil chemotaxis / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of protein secretion / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Assembly Of The HIV Virion / positive regulation of NF-kappaB transcription factor activity / Budding and maturation of HIV virion / platelet activation / platelet aggregation / integrin binding / positive regulation of protein phosphorylation / neuron differentiation / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / Platelet degranulation / protein folding / cellular response to oxidative stress / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / focal adhesion / apoptotic process / Neutrophil degranulation / protein-containing complex / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKeedy, D.A. / Kenner, L.R. / Warkentin, M. / Woldeyes, R.A. / Thompson, M.C. / Brewster, A.S. / Van Benschoten, A.H. / Baxter, E.L. / Hopkins, J.B. / Uervirojnangkoorn, M. ...Keedy, D.A. / Kenner, L.R. / Warkentin, M. / Woldeyes, R.A. / Thompson, M.C. / Brewster, A.S. / Van Benschoten, A.H. / Baxter, E.L. / Hopkins, J.B. / Uervirojnangkoorn, M. / McPhillips, S.E. / Song, J. / Mori, R.A. / Holton, J.M. / Weis, W.I. / Brunger, A.T. / Soltis, M. / Lemke, H. / Gonzalez, A. / Sauter, N.K. / Cohen, A.E. / van den Bedem, H. / Thorne, R.E. / Fraser, J.S.
CitationJournal: Elife / Year: 2015
Title: Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography.
Authors: Keedy, D.A. / Kenner, L.R. / Warkentin, M. / Woldeyes, R.A. / Hopkins, J.B. / Thompson, M.C. / Brewster, A.S. / Van Benschoten, A.H. / Baxter, E.L. / Uervirojnangkoorn, M. / McPhillips, S.E. ...Authors: Keedy, D.A. / Kenner, L.R. / Warkentin, M. / Woldeyes, R.A. / Hopkins, J.B. / Thompson, M.C. / Brewster, A.S. / Van Benschoten, A.H. / Baxter, E.L. / Uervirojnangkoorn, M. / McPhillips, S.E. / Song, J. / Alonso-Mori, R. / Holton, J.M. / Weis, W.I. / Brunger, A.T. / Soltis, S.M. / Lemke, H. / Gonzalez, A. / Sauter, N.K. / Cohen, A.E. / van den Bedem, H. / Thorne, R.E. / Fraser, J.S.
History
DepositionMar 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase A


Theoretical massNumber of molelcules
Total (without water)18,0371
Polymers18,0371
Non-polymers00
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.423, 51.817, 87.955
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase A / PPIase A / Cyclophilin A / Cyclosporin A-binding protein / Rotamase A


Mass: 18036.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIA, CYPA / Production host: Escherichia coli (E. coli) / References: UniProt: P62937, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 71

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Crystals were grown by mixing equal volumes of well solution (100 mM HEPES pH 7.5, 23% PEG 3350, 5 mM TCEP) and protein (60 mg/mL in 20 mM HEPES pH 7.5, 100 mM NaCl, 0.5 mM TCEP) in the hanging-drop format.

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Data collection

DiffractionMean temperature: 273 K
Ambient temp details: Crystals were coated with paratone oil immediately after looping and mounted on the goniometer.
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: XPP / Wavelength: 1.31 Å
DetectorType: RAYONIX MX325HE / Detector: CCD / Date: May 16, 2014 / Details: 2013-12-16 - Second data collection date
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.31 Å / Relative weight: 1
ReflectionResolution: 1.75→43.98 Å / Num. obs: 19942 / % possible obs: 99 % / Redundancy: 23.88 % / Net I/σ(I): 26.03
Reflection shellResolution: 1.75→1.81 Å / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
cctbx.xfeldata reduction
cctbx.primedata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CPL

2cpl


Resolution: 1.75→43.978 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 2.41 / Phase error: 27.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2489 625 3.14 %
Rwork0.2002 --
obs0.2017 19936 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→43.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1258 0 0 198 1456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171616
X-RAY DIFFRACTIONf_angle_d1.4372197
X-RAY DIFFRACTIONf_dihedral_angle_d13.223614
X-RAY DIFFRACTIONf_chiral_restr0.071221
X-RAY DIFFRACTIONf_plane_restr0.008299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.92610.36121510.34284660X-RAY DIFFRACTION97
1.9261-2.20480.28641540.25414765X-RAY DIFFRACTION99
2.2048-2.77780.26891560.21254859X-RAY DIFFRACTION99
2.7778-43.99150.20781640.15365027X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.58860.0393-0.77631.1849-0.03542.4630.0015-0.05220.00240.02460.015-0.07030.03940.1316-0.01720.13730.0096-0.00240.15320.00180.15176.308610.864212.472
24.73582.5942-4.53412.471-1.58295.1262-0.16130.024-0.1544-0.01330.0674-0.16490.43480.07260.09760.19040.0009-0.02790.19560.02740.13342.41072.347413.418
34.21920.45632.87571.3124-1.42326.10680.1508-0.4399-0.10520.20740.01220.03790.1648-0.5789-0.1140.17530.02190.00170.1602-0.0050.1785-4.639710.222118.3032
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 2:124
2X-RAY DIFFRACTION2chain A and resseq 125:142
3X-RAY DIFFRACTION3chain A and resseq 143:165

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